ConvertDropSeqfolders: ConvertDropSeqfolders

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

ConvertDropSeqfolders

Description

This function takes a parent directory with a number of subfolders, each containing the standard output of 10X Cell Ranger. It (1) loads the filtered data matrices, (2) converts them to Seurat objects, and (3) saves them as .RDS files.

Usage

ConvertDropSeqfolders(
  InputDir,
  folderPattern = "SRR*",
  filePattern = "expression.tsv.gz",
  useVroom = TRUE,
  col_types.vroom = list(GENE = "c", .default = "d"),
  min.cells = 10,
  min.features = 200,
  updateHGNC = TRUE,
  ShowStats = TRUE,
  minDimension = 10,
  overwrite = FALSE
)

Arguments

InputDir	A character string specifying the input directory.
folderPattern	A character string specifying the pattern of folder names to be searched. Default: 'SRR*'.
filePattern	A character string specifying the pattern of file names to be searched. Default: 'expression.tsv.gz'.
useVroom	A logical value indicating whether to use vroom. Default: TRUE.
col_types.vroom	A list defining column types for vroom. Default: list("GENE" = "c", .default = "d").
min.cells	An integer value specifying the minimum number of cells. Default: 10.
min.features	An integer value specifying the minimum number of features. Default: 200.
updateHGNC	A logical value indicating whether to update the HGNC. Default: TRUE.
ShowStats	A logical value indicating whether to show statistics. Default: TRUE.
minDimension	An integer value specifying the minimum dimension. Default: 10.
overwrite	A logical value indicating whether to overwrite files. Default: FALSE.

See Also

vroom read_delim

Examples

## Not run: 
if (interactive()) {
  ConvertDropSeqfolders(InputDir = InputDir)
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.